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General Information
Symbol
Dmel\Trf2
Species
D. melanogaster
Name
TATA box binding protein-related factor 2
Annotation Symbol
CG18009
Feature Type
FlyBase ID
FBgn0261793
Gene Model Status
Stock Availability
Gene Summary
TATA box binding protein-related factor 2 (Trf2) encodes a core promoter recognition factor that mediates gene transcription. It contributes to spiracle morphogenesis, pupal development and salivary gland cell death. [Date last reviewed: 2019-08-01] (FlyBase Gene Snapshot)
Also Known As

dTRF2, TLF

Key Links
Genomic Location
Cytogenetic map
Sequence location
Recombination map
1-23
RefSeq locus
NC_004354 REGION:8409272..8433011
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (21 terms)
Molecular Function (7 terms)
Terms Based on Experimental Evidence (6 terms)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
Biological Process (8 terms)
Terms Based on Experimental Evidence (6 terms)
CV Term
Evidence
References
inferred from direct assay
involved_in pupal development
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
inferred from mutant phenotype
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
inferred from biological aspect of ancestor with PANTHER:PTN000013136
(assigned by GO_Central )
Cellular Component (6 terms)
Terms Based on Experimental Evidence (5 terms)
CV Term
Evidence
References
inferred from direct assay
located_in heterochromatin
inferred from direct assay
inferred from direct assay
inferred from direct assay
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from sequence or structural similarity with HGNC:11588
inferred from sequence or structural similarity with SGD:S000000950
Protein Family (UniProt)
-
Summaries
Gene Snapshot
TATA box binding protein-related factor 2 (Trf2) encodes a core promoter recognition factor that mediates gene transcription. It contributes to spiracle morphogenesis, pupal development and salivary gland cell death. [Date last reviewed: 2019-08-01]
Gene Group (FlyBase)
TATA-BINDING PROTEIN AND TBP-RELATED FACTORS -
The TATA-binding protein-related factors (TRFs) and TATA-binding protein (TBP) are similar in sequence sharing a 180 amino acid saddle-shaped DNA binding core domain. TBP is required by all three RNA polymerases and was considered a universal transcription factor. Subsequently, metazoan TRFs were shown to mediate transcription independently of TBP and to regulate the expression of specific sets of genes. (Adapted from FBrf0162294, FBrf0131150 and FBrf0229757).
Summary (Interactive Fly)

differentially recognizes and regulates a subset of TATA-less promoters

Gene Model and Products
Number of Transcripts
6
Number of Unique Polypeptides
3

Please see the JBrowse view of Dmel\Trf2 for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)
Isoform displayed:
Pfam protein domains
InterPro name
classification
start
end
Protein Domains (via SMART)
Isoform displayed:
SMART protein domains
InterPro name
classification
start
end
Comments on Gene Model

Low-frequency RNA-Seq exon junction(s) not annotated.

Tissue-specific extension of 3' UTRs observed during later stages (FBrf0218523, FBrf0219848); all variants may not be annotated

Gene model reviewed during 5.46

Apparent intron within coding exon in cDNA GB:AY069554 (LD27895) is likely to be an artifact; possibly caused by reverse transcriptase template-switching in regions of CAG repeats.

Gene model reviewed during 5.44

Annotated transcripts do not represent all supported alternative splices within 5' UTR.

Gene model reviewed during 6.04

Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0112927
7131
1715
FBtr0300577
9866
1715
FBtr0330105
6840
1715
FBtr0330106
10041
632
FBtr0333750
7034
1714
FBtr0333811
6934
632
Additional Transcript Data and Comments
Reported size (kB)

3.9 (longest cDNA)

Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0111840
194.7
1715
4.64
FBpp0289804
194.7
1715
4.64
FBpp0303138
194.7
1715
4.64
FBpp0303139
68.5
632
8.04
FBpp0305892
194.6
1714
4.65
FBpp0305945
68.5
632
8.04
Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

1715 aa isoforms: Trf2-PE, Trf2-PF, Trf2-PG
632 aa isoforms: Trf2-PH, Trf2-PJ
Additional Polypeptide Data and Comments
Reported size (kDa)

632 (aa); 68 (kD predicted)

Comments
External Data
Crossreferences
InterPro - A database of protein families, domains and functional sites
Linkouts
Sequences Consistent with the Gene Model
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Trf2 using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Expression Data
Expression Summary Ribbons
Colored tiles in ribbon indicate that expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.
Transcript Expression
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data

Expression pattern inferred from unspecified enhancer trap line.

Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data

Trf2 protein is detected in the female germline but not in somatic cells. It is detected in the germline stem cells in the apical part of the germarium, in cystoblasts, in cyst cells in the distal part of the germarium, and in the nuclei of nurse cells and the oocyte in egg chambers. During spermatogenesis, Trf2 protein is first detected in the nuclei of young primary spermatocytes and reaches a peak in mature primary spermatocytes. It then gradually decreases and is not detected in spermatids.

Marker for
 
Subcellular Localization
CV Term
Evidence
References
inferred from direct assay
located_in heterochromatin
inferred from direct assay
inferred from direct assay
inferred from direct assay
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Trf2 in GBrowse 2
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Reference
See Gelbart and Emmert, 2013 for analysis details and data files for all genes.
Developmental Proteome: Life Cycle
Developmental Proteome: Embryogenesis
External Data and Images
Linkouts
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Images
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 47 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 19 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Trf2
Transgenic constructs containing regulatory region of Trf2
Aberrations (Deficiencies and Duplications) ( 1 )
Alleles Representing Disease-Implicated Variants
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
Sterility
Allele
Other Phenotypes
Allele
Phenotype manifest in
Allele
nuclear chromosome & salivary gland, with Scer\GAL42314
nucleus & salivary gland, with Scer\GAL42314
Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (3)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
9 of 15
Yes
Yes
2 of 15
No
No
8  
2 of 15
No
No
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (3)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
9 of 15
Yes
Yes
2 of 15
No
No
1 of 15
No
No
Rattus norvegicus (Norway rat) (3)
6 of 13
Yes
Yes
2 of 13
No
No
2 of 13
No
No
Xenopus tropicalis (Western clawed frog) (4)
8 of 12
Yes
Yes
2 of 12
No
No
2 of 12
No
No
1 of 12
No
Yes
Danio rerio (Zebrafish) (3)
9 of 15
Yes
Yes
2 of 15
No
No
2 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (2)
5 of 15
Yes
Yes
1 of 15
No
No
Arabidopsis thaliana (thale-cress) (2)
2 of 9
Yes
No
2 of 9
Yes
No
Saccharomyces cerevisiae (Brewer's yeast) (1)
3 of 15
Yes
No
Schizosaccharomyces pombe (Fission yeast) (1)
2 of 12
Yes
No
Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG0919026L )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila suzukii
Spotted wing Drosophila
Drosophila simulans
Drosophila sechellia
Drosophila sechellia
Drosophila erecta
Drosophila yakuba
Drosophila ananassae
Drosophila pseudoobscura pseudoobscura
Drosophila persimilis
Drosophila willistoni
Drosophila virilis
Drosophila mojavensis
Drosophila mojavensis
Drosophila grimshawi
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG09150AK8 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Glossina morsitans
Tsetse fly
Mayetiola destructor
Hessian fly
Aedes aegypti
Yellow fever mosquito
Anopheles darlingi
American malaria mosquito
Anopheles gambiae
Malaria mosquito
Anopheles gambiae
Malaria mosquito
Culex quinquefasciatus
Southern house mosquito
Culex quinquefasciatus
Southern house mosquito
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W0CQ9 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Danaus plexippus
Monarch butterfly
Heliconius melpomene
Postman butterfly
Apis florea
Little honeybee
Apis mellifera
Western honey bee
Bombus impatiens
Common eastern bumble bee
Bombus terrestris
Buff-tailed bumblebee
Linepithema humile
Argentine ant
Megachile rotundata
Alfalfa leafcutting bee
Nasonia vitripennis
Parasitic wasp
Dendroctonus ponderosae
Mountain pine beetle
Tribolium castaneum
Red flour beetle
Pediculus humanus
Human body louse
Rhodnius prolixus
Kissing bug
Cimex lectularius
Bed bug
Acyrthosiphon pisum
Pea aphid
Acyrthosiphon pisum
Pea aphid
Zootermopsis nevadensis
Nevada dampwood termite
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0CO7 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Ixodes scapularis
Black-legged tick
Stegodyphus mimosarum
African social velvet spider
Tetranychus urticae
Two-spotted spider mite
Daphnia pulex
Water flea
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0K64 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Ciona intestinalis
Vase tunicate
Gallus gallus
Domestic chicken
Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (4)
4 of 10
3 of 10
3 of 10
2 of 10
Human Disease Associations
FlyBase Human Disease Model Reports
    Disease Model Summary Ribbon
    Disease Ontology (DO) Annotations
    Models Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Evidence
    References
    Potential Models Based on Orthology ( 0 )
    Human Ortholog
    Disease
    Evidence
    References
    Modifiers Based on Experimental Evidence ( 0 )
    Allele
    Disease
    Interaction
    References
    Disease Associations of Human Orthologs (via DIOPT v8.0 and OMIM)
    Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
    Homo sapiens (Human)
    Gene name
    Score
    OMIM
    OMIM Phenotype
    DO term
    Complementation?
    Transgene?
    Functional Complementation Data
    Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.
    Interactions
    Summary of Physical Interactions
    Summary of Genetic Interactions
    esyN Network Diagram
    esyN Network Key:
    Suppression
    Enhancement

    Please look at the allele data for full details of the genetic interactions
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    Starting gene(s)
    Interaction type
    Interacting gene(s)
    Reference
    External Data
    Linkouts
    DroID - A comprehensive database of gene and protein interactions.
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Pathways
    Signaling Pathways (FlyBase)
    Metabolic Pathways
    External Data
    Linkouts
    KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    X
    Recombination map
    1-23
    Cytogenetic map
    Sequence location
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    7E3-7E6
    Left limit from in situ hybridisation (FBrf0125103) Right limit from in situ hybridisation (FBrf0125103); Left limit from in situ hybridisation (FBrf0107552) Right limit from in situ hybridisation (FBrf0107552)
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    7E-7E
    (determined by in situ hybridisation)
    7E3-7E11
    (determined by in situ hybridisation)
    7E5-7E6
    (determined by in situ hybridisation)
    Experimentally Determined Recombination Data
    Location
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (23)
    Genomic Clones (25)
    cDNA Clones (54)
     

    Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see GBrowse for alignment of the cDNAs and ESTs to the gene model.

    cDNA clones, fully sequenced
    BDGP DGC clones
    Other clones
      Drosophila Genomics Resource Center cDNA clones

      For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

      cDNA Clones, End Sequenced (ESTs)
      BDGP DGC clones
      RNAi and Array Information
      Linkouts
      DRSC - Results frm RNAi screens
      GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
      Antibody Information
      Laboratory Generated Antibodies
      Commercially Available Antibodies
       
      Other Information
      Relationship to Other Genes
      Source for database identify of
      Source for database merge of

      Source for merge of: Trf2 CG18009

      Source for merge of: Trf2 l(1)G0039 l(1)G0295 l(1)G0425 l(1)G0071

      Additional comments

      "l(1)G0295" may affect "Trf2". "l(1)G0425" may affect "Trf2". "l(1)G0039" may affect "Trf2". "l(1)G0219" may affect "Trf2". "l(1)G0228" may affect "Trf2". "l(1)G0356" may affect "Trf2". "l(1)G0096" may affect "Trf2". "l(1)G0332" may affect "Trf2". "l(1)G0166" may affect "Trf2". "l(1)G0372" may affect "Trf2". "l(1)G0178" may affect "Trf2". "l(1)G0376" may affect "Trf2". "l(1)G0071" may affect "Trf2". "l(1)G0424" may affect "Trf2".

      "l(1)G0039" may affect "Trf2".

      "l(1)G0295" may affect "Trf2".

      "l(1)G0425" may affect "Trf2".

      "l(1)G0071" may affect "Trf2".

      Other Comments

      Nonsense-mediated mRNA decay (NMD) down-regulates a distinct splice isoform(s) of this gene.

      Origin and Etymology
      Discoverer
      Etymology
      Identification
      External Crossreferences and Linkouts ( 66 )
      Sequence Crossreferences
      NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
      GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.
      GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
      RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
      UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
      Other crossreferences
      BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
      Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
      DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
      EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
      Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
      FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
      FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
      Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
      FlyMine - An integrated database for Drosophila genomics
      GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
      iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
      InterPro - A database of protein families, domains and functional sites
      KEGG Genes - Molecular building blocks of life in the genomic space.
      MARRVEL_MODEL - MARRVEL (model organism gene)
      modMine - A data warehouse for the modENCODE project
      Linkouts
      DroID - A comprehensive database of gene and protein interactions.
      DRSC - Results frm RNAi screens
      Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
      KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
      MIST (protein-protein) - An integrated Molecular Interaction Database
      Synonyms and Secondary IDs (25)
      Reported As
      Symbol Synonym
      l(1)G0039
      l(1)G0071
      l(1)G0295
      l(1)G0425
      Name Synonyms
      TATA box binding protein-related factor 2
      TATA box-binding protein related factor 2
      TBP related factor 2
      TBP-like factor
      TBP-related factor 2
      lethal (1) G0039
      lethal (1) G0071
      lethal (1) G0295
      lethal (1) G0425
      Secondary FlyBase IDs
      • FBgn0026758
      • FBgn0026762
      • FBgn0030036
      • FBgn0026705
      • FBgn0040181
      • FBgn0040163
      • FBgn0026688
      Datasets (0)
      Study focus (0)
      Experimental Role
      Project
      Project Type
      Title
      References (119)